Cellular reprogramming and ageing

 

Understanding and controlling cell state transitions

The lab’s research is centred around the in-depth profiling of transcriptional and epigenetic changes that occur during cellular transitions, to understand their molecular basis and importantly, to control them. In this context, we study cell fate conversions that occur rapidly as a consequence of forced cellular reprogramming, as well as the subtler and slower, albeit functionally meaningful, changes that occurring as part of developmental maturation and during ageing.

Research overview

Transdifferentiation and induced pluripotent stem cell (iPSC) technologies are forms of transcription factor (TF)-mediated cell reprogramming. This is achieved by the overexpression of a set of key TFs in a given cell type to induce reprogramming into another cell type.

Age is one of the greatest risk factors for most degenerative diseases of mid- and late life and meaningful therapeutic control over the ageing process would be revolutionary. On a cellular level, ageing appears to be a largely epigenetic phenomenon that can be manipulated by pluripotency induction or transient expression of iPSC reprogramming factors.

As such, functionally compromised aged blood stem cells can be reprogrammed into iPSCs and used to generate young healthy animals with a normal hematopoietic system and (PMIDs: 28224997, 23476050). Accordingly, if we understand the cellular age-state with its associated epigenetic signature well enough, direct strategies might be implemented to edit cellular age without a need for pluripotency induction.

Among other things, the Nefzger lab investigates why youthful cell identity deteriorates over time and explores the use of transcription factors and epigenetic modifiers to directly covert aged cells towards a more functional state without affecting cell type identity.

Research Members

Traineeships, honours and PhD projects include:

  • The impact of ageing on the cellular identity network
  • Epigenetic fidelity in induced somatic and pluripotent stem cells
  • Editing the developmental stage of somatic stem cells

To discuss the group’s projects further, contact Dr Christian Nefzger, below.

Joseph Chen*, Christian M. Nefzger*#, Fernando J. Rossello, Yu B.Y. Sun, Sue Mei Lim, Xiaodong Liu, Suzan de Boer Anja S. Knaupp, Jinhua Li, Kathryn C. Davidson, Jose M. Polo#, Tiziano Barberi#. Fine tuning of canonical Wnt stimulation enhances differentiation of pluripotent stem cells independent of β-catenin-mediated TCF signaling. STEM CELLS. 2018 Jun;36(6):822-833. doi: 10.1002/stem.2794. Epub 2018 Feb 14.

 

Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger CM, Polo JM, Ford E, Lister R. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. GENOME RESEARCH. 2018 Aug;28(8):1193-1206. doi: 10.1101/gr.233049.117. Epub 2018 Jun 15.

 

Christian M. Nefzger*, Fernando J. Rossello*, Joseph Chen, Xiaodong Liu, Anja S. Knaupp, Jaber Firas, Jacob M. Paynter, Jahnvi Pflueger, Sam Buckberry, Sue Mei Lim, Brenda Williams, Sara Alaei, Keshav Faye-Chauhan, Enrico Petreto, Susan K. Nilsson, Ryan Lister, Mirana Ramialison, David R. Powel, Owen J.L. Rackham# and Jose M. Polo#. Cell type of origin dictates the route to pluripotency. CELL REPORTS. 2017 Dec 5;21(10):2649-2660. DOI: 10.1016/j.celrep.2017.11.029.

 

Anja S. Knaupp, Sam Buckberry, Jahnvi Pflueger, Sue Mei Lim, Ethan Ford, Michael R. Larcombe, Fernando J. Rossello, Alex de Mendoza, Sara Alaei, Jaber Firas, Melissa L. Holmes, Christian M. Nefzger, Ryan Lister# and Jose M. Polo#. Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming. CELL STEM CELL. 2017 Dec 7;21(6):834-845.e6. DOI: 10.1016/j.stem.2017.11.007.

 

Liu X*, Nefzger CM*, Rossello FJ, Chen J, Knaupp AS, Firas J, Ford E, Pflueger J, Paynter JM, Chy HS, O’Brien CM, Huang C, Mishra K, Hodgson-Garms M, Jansz N, Williams SM, Blewitt ME, Nilsson SK, Schittenhelm RB, Laslett AL, Lister R, Polo JM#. Comprehensive characterization of distinct states of human naïve pluripotency generated by reprogramming. NATURE METHODS, 2017 Nov;14(11):1055-1062. DOI: 10.1038/nmeth.4436.

 

Nefzger CM, Polo JM#. DEAD-Box RNA Binding Protein: Not a Black-Box during reprogramming. CELL STEM CELL. 2017 Apr 6;20(4):419-420. DOI: 10.1016/j.stem.2017.03.006.Alaei S, Knaupp AS, Lim SM, Chen J, Holmes ML, Änkö ML, Nefzger CM# and Polo JM#. An improved reprogrammable mouse model harboring the reverse tetracycline-controlled transcriptional transactivator 3. STEM CELL RESEARCH. 2016 Jul;17(1):49-53. DOI: 10.1016/j.scr.2016.05.008.

 

Nefzger CM*, Jarde T*, Horvay K, Knaupp AS, Rosello FJ, Chen J, Powel DR, Abud HE#, Polo JM#. A versatile strategy for isolating a highly enriched population of intestinal stem cells. STEM CELL REPORTS. 2016 Mar 8;6(3):321-9. DOI: 10.1016/j.stemcr.2016.01.014.

 

Owen J.L. Rackham*, Jaber Firas*, Hai Fang, Matt E. Oates, Melissa Holmes, Anja Knaupp, the fantom consortium, Harukazu Suzuki, Christian M Nefzger, Carsten O. Daub, Jay W. Shin,Enrico Petretto, Alistair R.R. Forrest, Yoshihide Hayashizaki, Jose M. Polo#, Julian Gough#. Mogrify: An Atlas for Direct Reprogramming Between Human Cell Types. NATURE GENETICS. 2016. 2016 Mar;48(3):331-5. DOI: 10.1038/ng.3487.

 

Firas J*, Liu X*, Nefzger CM# and Polo JM#. GM-CSF and MEF-conditioned media support feeder-free reprogramming of mouse granulocytes to iPS cells. DIFFERENTIATION. 2014 Jun;87(5):193-9. DOI: 10.1016/j.diff.2014.05.003.

 

Polo JM*, Anderssen E*, Walsh RM, Schwarz BA, Nefzger CM, Lim SM, Borkent M, Apostolou E, Alaei S, Cloutier J, Bar-Nur O, Cheloufi S, Stadtfeld M, Figueroa ME, Robinton D, Natesan S, Melnick A, Zhu J, Ramaswamy S#, Hochedlinger K#. A molecular roadmap of reprogramming somatic cells into iPS cells. CELL. 2012 Dec 21;151(7):1617-32. DOI: 10.1016/j.cell.2012.11.039.

 

Nefzger CM*, Su CT*, Fabb SR, Hartley BJ, Beh SJ, Zeng WR, Haynes JM#, Pouton CW#. Lmx1a allows context-specific isolation of progenitors of GABAergic or dopaminergic neurons during neural differentiation of embryonic stem cells. STEM CELLS. 2012 Jul;30(7):1349-61. DOI: 10.1002/stem.1105.

 

Dr Nefzger is currently a group leader in the Division of Cell Biology and and Molecular Medicine at the Institute for Molecular Bioscience. He has published in numerous academic journals including 10 first and 6 corresponding author publications in renowned journals like Nature Methods, Cell Reports, Cell Stem Cells, Stem Cell Reports, Stem Cells and Stem Cell Research. Middle author publications in journals include Cell, Nature Immunology, Nature Genetics, Cell Stem Cells, Molecular Cell, Nature Communications, Immunity, EMBO Journal, eLIFE and Stem Cells.

While essentially all cells in our bodies share the same genome, different gene sets are active in each cell type. A breakthrough for regenerative medicine was the discovery that somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs, 2016). iPSCs can give rise to any cell type of the body and as such hold tremendous potential for drug screening and personalised cell replacement therapies. However, a lack of basic knowledge about reprogramming and its differentiation process have hampered clinical translation for patients. Dr Nefzger’s research helped shape the current understanding of the molecular mechanisms underpinning cellular reprogramming, thereby revealing strategies that make the process more efficient (Nefzger et al. Cell Reports, 2017, Liu and Nefzger et al. Nat Methods 2017, Knaupp et al, CSC 2017, Polo et al., Cell 2012). Furthermore, he established novel guided cell fate transitions using transcription factors (Liu and Nefzger et al. Nat Methods 2017, Rackham et al., Nat Genetics 2016, Nefzger et al. Stem Cells 2011, Nefzger et al. Stem Cells, 2012). He has received research funding from the NHMRC, Monash University (e.g. in the form of strategic grant scheme awards: ECP009, ECD0200, SGS17-0696) and the University of Queensland.

Significance, innovation and international reach of his work is evidenced by 30 papers with >1440 citations cross 51 countries and 6 subject fields. Media uptake, nationally and internationally (e.g. Scimex, ScienceDaily, EurekaAlert for Nefzger et al., Cell Reports, 2017 & Liu and Nefzger et al., Nature Methods, 2017), demonstrates broad public outreach of his work. Recognition is reflected by presentations at prestigious conferences, including the leading national & international stem cell meetings, ASSCR and ISSCR, respectively, precipitating award for best ERC presentation at the 2016 ASSCR meeting. Dr Nefzger has also presented at renowned field-spanning conferences like ComBio 2016 and the Cell Press Symposium on Aging and Metabolism 2018. 

Dr Nefzger is very passionate and actively involvement in setting-up and maintaining state of the art technology platforms. As such he is co-director of the Queensland Facility of Advanced Genome Editing (QFAGE - formerly affiliated with the Genome Innovation Hub), offering CRISPR/Cas9-based services for the generation of genetically modified mice and cell lines. His past work was leveraged to help establish the Fluidigm Single Cell Centre of Excellence at the Monash Health Translational Precinct as a service hub for the local scientific community. Dr Nefzger was part of Monash University’s FlowCore (cell sorting facility) review panel to instigate new user policies and help decide on the procurement of new equipment. Furthermore, he is supporting an initiative lead by the Pro-Vice-Chancellor for Research Infrastructure (UQ) with the aim of establishing a centralised flow cytometry facility at the St Lucia campus.

Dr Nefzger has mentored 29 students and is currently main supervisor of two Master’s students at UQ (Ying Yang, Quijie Zhu) and co-supervisor of 3 PhD students (Ming Tran, UQ; Xiaodong Liu, Monash University; Eva Chan, Monash University). His students and former staff have received awards, including the Carmela and Carmelo Ridolfo Prize in Stem Cell Research (Jaber Firas and Xiadong Liu), and have orally presented their work at numerous conferences including the 2018 and 2019 ISSCR meetings (Joseph Chen; Xiaodong Liu). Dr Nefzger is a frequent member of Research High Degree (RHD) Student Confirmation Committees to assess progression of RHD students (e.g. Ziyi Huang, Monash University; Enakshi Sinnia, UQ). He is also actively engaged in communications with the general public. In 2013, 2015 and 2017 he provided five-day supervised lab experience for groups of three year-11 students (Sir John Monash high school). In 2015 he mentored a year-12 student (Gregory Goldstein, Sir John Monash high school) as part of a support program for high achieving students.

Dr Nefzger has lectured as part of the Monash University's BMS3031 Masterclass (Stem Cells, Development and Commercialization) and covered cell fate conversion at the Monash Medical Centre (MCR 5100 course) 2016-2019. To help promote ageing research he organised and chaired the successful UQ Biology of Ageing symposium (2019), showcasing prominent international speaker and local researchers.

We collaborate nationally and internationally, and across research fields.

Collaborators include:

  • Susie Nilsson, CSIRO, Melbourne, Australia
  • Helen Abud, Monash University, Melbourne, Australia
  • Owen Rackham, Duke NUS, Singapore
  • Jose Polo, Monash University, Melbourne, Australia
  • Ryan Lister, University of Western Australia, Perth, Australia
  • Quan Nguyen, IMB, University of Queensland, Brisbane, Australia
  • Nathan Palpant, IMB, University of Queensland, Brisbane, Australia

2018-2020 NHMRC Project Grant (sole CI, APP1146623) - Generation of human intestinal stem cells by direct reprogramming from somatic and pluripotent cell sources.

 

Contact

Dr Chrisitan Nefzger
Senior Research Fellow
Group Leader

  c.nefzger@imb.uq.edu.au
  IMB Researcher Profile
  Google Scholar profile